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KastanDay / ML4Bio

LLMs to execute Bioinformatics workflows, esp. RNA-seq
MIT License
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Create the workflow in python notebook for RNA-Seq on PBMC Samples and create a PR to the main branch. #6

Open rohan-uiuc opened 10 months ago

rohan-uiuc commented 10 months ago

Experiment Type: RNA-Seq Sequencing of total cellular RNA

Workflow Management: Bash/SLURM Scripting and job scheduling

Software Stack: FastQC MultiQC STAR RSEM samtools DESeq2

What else to know about the pipeline? I am working PBMC samples collected from patients that are undergoing immunotherapy. Use the report available at ⭐️____Report_Antonson_WholeBrain_2022Mar.html for reproducing results and getting insights about steps.

lil-jr-dev[bot] commented 10 months ago

Thanks for opening a new issue! I'll now try to finish this implementation and open a PR for you to review. I'll comment if I get blocked or 'request your review' if I think I'm successful. So just watch for emails while I work. Please comment to give me additional instructions.

lil-jr-dev[bot] commented 10 months ago

Inputs conda install -c bioconda bioconductor-deseq2 to tool {'name': 'terminal', 'description': 'Run shell commands on this MacOS machine.'} were rejected.

lil-jr-dev[bot] commented 10 months ago

Thanks for opening a new issue! I'll now try to finish this implementation and open a PR for you to review. I'll comment if I get blocked or 'request your review' if I think I'm successful. So just watch for emails while I work. Please comment to give me additional instructions.

lil-jr-dev[bot] commented 10 months ago

Thanks for opening a new issue! I'll now try to finish this implementation and open a PR for you to review. I'll comment if I get blocked or 'request your review' if I think I'm successful. So just watch for emails while I work. Please comment to give me additional instructions.

lil-jr-dev[bot] commented 10 months ago

list index out of range

lil-jr-dev[bot] commented 10 months ago

Thanks for opening a new issue! I'll now try to finish this implementation and open a PR for you to review. I'll comment if I get blocked or 'request your review' if I think I'm successful. So just watch for emails while I work. Please comment to give me additional instructions.

lil-jr-dev[bot] commented 10 months ago

list index out of range

lil-jr-dev[bot] commented 10 months ago

Thanks for opening a new issue! I'll now try to finish this implementation and open a PR for you to review. I'll comment if I get blocked or 'request your review' if I think I'm successful. So just watch for emails while I work. Please comment to give me additional instructions.

lil-jr-dev[bot] commented 10 months ago

Thanks for opening a new issue! I'll now try to finish this implementation and open a PR for you to review. I'll comment if I get blocked or 'request your review' if I think I'm successful. So just watch for emails while I work. Please comment to give me additional instructions.

lil-jr-dev[bot] commented 10 months ago

Inputs jupyter notebook to tool {'name': 'terminal', 'description': 'Run shell commands on this MacOS machine.'} were rejected.